genomation protocols

genomation specifications

Information


Unique identifier OMICS_02306
Name genomation
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License Artistic License version 2.0
Computer skills Advanced
Version 1.11.13
Stability Stable
Requirements grid
Maintained Yes

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Documentation


Maintainers


  • person_outline Christopher E. Mason <>
  • person_outline genomation <>
  • person_outline Altuna Akalin <>
  • person_outline Dirk Schubeler <>

Publication for genomation

genomation IN pipeline

2017
PMCID: 5487215
PMID: 28653622
DOI: 10.7554/eLife.23203.062

[…] transcription factor binding sites (tfbs), and well positioned nucleosomes was calculated across the 2 kb regions centered on the middle of these regions using the scorematrixbin function in the genomation package (akalin et al., 2015) in r (r core team, 2015). data were aggregated in 5 bp bins for each region and across all regions covered in a single cell. the average methylation level […]

genomation institution(s)
Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland; Bioinformatics Group, Department of Molecular Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia; Department of Physiology and Biophysics and the Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY, USA; Faculty of Science, University of Basel, Basel, Switzerland; Department of Informatics, University of Oslo, Oslo, Norway
genomation funding source(s)
Supported by the Novartis Research Foundation, the European Union [NoE ‘EpiGeneSys’ FP7- HEALTH-2010-257082 and the ‘Blueprint’ consortium FP7-282510], the European Research Council (EpiGePlas) and the Swiss initiative in Systems Biology (RTD Cell Plasticity), EC Seventh Framework Program [Integra-Life grant 315997], EMBO Young Investigator Program [installation grant 1431/2006] and Croatian MSES [grant 119-0982913-1211].

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